Hey, I got these errors after submitting. The file is zipped so I guess the format should be right. Could anyone kindly give me pointers how to solve this? Regards, Duc ``` STDERR: 2024-08-28T19:56:19.691936522Z 86364909acc8 2024-08-28 19:56:19,691 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/workflow.cwl' STDERR: 2024-08-28T19:56:26.809092397Z 86364909acc8 2024-08-28 19:56:26,808 MainThread WARNING cwltool: Workflow checker warning: STDERR: 2024-08-28T19:56:26.809160698Z MIDI-B-De-identification-main/workflow.cwl:78:9: Source 'filepath' of type ["null", "File"] may be STDERR: 2024-08-28T19:56:26.809171837Z incompatible STDERR: 2024-08-28T19:56:26.809178068Z MIDI-B-De-identification-main/workflow.cwl:86:9: with sink 'compressed_file' of type "File" STDERR: 2024-08-28T19:56:29.275184475Z 86364909acc8 2024-08-28 19:56:29,274 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2024-08-28T19:56:30.518412671Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmp_u0zp20_/worker_log.txt STDERR: 2024-08-28T19:56:30.901351272Z 86364909acc8 2024-08-28 19:56:30,900 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run STDERR: 2024-08-28T19:56:30.902709522Z 86364909acc8 2024-08-28 19:56:30,902 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_set_permissions.cwl/instance-izy25ewx with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2024-08-28T19:56:30.902941571Z 86364909acc8 2024-08-28 19:56:30,902 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_set_permissions.cwl/instance-u_7emo5q with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2024-08-28T19:56:30.903171317Z 86364909acc8 2024-08-28 19:56:30,902 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-y6liu2dp with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2024-08-28T19:56:32.804380305Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpcy74kkac/worker_log.txt STDERR: 2024-08-28T19:56:32.871101923Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpczypf1lo/worker_log.txt STDERR: 2024-08-28T19:56:33.021027994Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpvzaoix0p/worker_log.txt STDERR: 2024-08-28T19:56:38.094081289Z 86364909acc8 2024-08-28 19:56:38,092 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_set_permissions.cwl/instance-u_7emo5q STDERR: 2024-08-28T19:56:38.488262142Z 86364909acc8 2024-08-28 19:56:38,487 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_set_permissions.cwl/instance-izy25ewx STDERR: 2024-08-28T19:58:05.512507443Z 86364909acc8 2024-08-28 19:58:05,511 Thread-48 WARNING toil.statsAndLogging: Got message from job at time 08-28-2024 19:58:05: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-9tm9gzvl/cleanup/file-vxdkna89/stream used 395.34% (4.0 GB [4248846336B] used, 1.0 GB [1074741824B] requested) at the end of its run. STDERR: 2024-08-28T19:58:06.038999477Z 86364909acc8 2024-08-28 19:58:06,037 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-y6liu2dp STDERR: 2024-08-28T19:58:06.039049444Z 86364909acc8 2024-08-28 19:58:06,038 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 15.6 G STDERR: 2024-08-28T19:58:07.222925849Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/worker_log.txt STDERR: 2024-08-28T19:58:48.270297721Z 86364909acc8 2024-08-28 19:58:48,269 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx STDERR: 2024-08-28T19:58:48.271103673Z 86364909acc8 2024-08-28 19:58:48,270 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx STDERR: 2024-08-28T19:58:48.271496426Z 86364909acc8 2024-08-28 19:58:48,271 MainThread WARNING toil.leader: Log from job kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx follows: STDERR: 2024-08-28T19:58:48.271551486Z =========> STDERR: 2024-08-28T19:58:48.271560067Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2024-08-28T19:58:48.271580770Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2024-08-28T19:58:48.271588705Z [job test.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2024-08-28T19:58:48.271594810Z WARNING:cwltool:[job test.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2024-08-28T19:58:48.271600927Z [job test.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tg_31agt3/tmp-outfrh1rggt$ docker \ STDERR: 2024-08-28T19:58:48.271607213Z run \ STDERR: 2024-08-28T19:58:48.271612765Z -i \ STDERR: 2024-08-28T19:58:48.271621306Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tg_31agt3/tmp-outfrh1rggt,target=/hEfyPh \ STDERR: 2024-08-28T19:58:48.271627989Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/txf0dx03b4dpmyuzm,target=/tmp \ STDERR: 2024-08-28T19:58:48.271673688Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tmpabgei983.tmp,target=/var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124,readonly \ STDERR: 2024-08-28T19:58:48.271681930Z --workdir=/hEfyPh \ STDERR: 2024-08-28T19:58:48.271687517Z --read-only=true \ STDERR: 2024-08-28T19:58:48.271692915Z --user=0:0 \ STDERR: 2024-08-28T19:58:48.271698427Z --rm \ STDERR: 2024-08-28T19:58:48.271704038Z --env=TMPDIR=/tmp \ STDERR: 2024-08-28T19:58:48.271709605Z --env=HOME=/hEfyPh \ STDERR: 2024-08-28T19:58:48.271715323Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/txf0dx03b5lbr_ftj/20240828195807-371422.cid \ STDERR: 2024-08-28T19:58:48.271721686Z docker.synapse.org/syn53065762/validate_score:v12 \ STDERR: 2024-08-28T19:58:48.271727258Z /bin/bash \ STDERR: 2024-08-28T19:58:48.271732853Z -c \ STDERR: 2024-08-28T19:58:48.271738373Z 'python /usr/local/bin/MIDI_validation_script/run_validation.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 && STDERR: 2024-08-28T19:58:48.271744708Z python /usr/local/bin/MIDI_validation_script/run_reports.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 # && STDERR: 2024-08-28T19:58:48.271788360Z # mkdir dciodvfy && STDERR: 2024-08-28T19:58:48.271797270Z # python /usr/local/bin/MIDI_validation_script/run_dciodvfy.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124' \ STDERR: 2024-08-28T19:58:48.271803725Z /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 STDERR: 2024-08-28T19:58:48.271809456Z INFO:cwltool:[job test.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tg_31agt3/tmp-outfrh1rggt$ docker \ STDERR: 2024-08-28T19:58:48.271815646Z run \ STDERR: 2024-08-28T19:58:48.271820697Z -i \ STDERR: 2024-08-28T19:58:48.271825849Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tg_31agt3/tmp-outfrh1rggt,target=/hEfyPh \ STDERR: 2024-08-28T19:58:48.271832458Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/txf0dx03b4dpmyuzm,target=/tmp \ STDERR: 2024-08-28T19:58:48.271839627Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tmpabgei983.tmp,target=/var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124,readonly \ STDERR: 2024-08-28T19:58:48.271846211Z --workdir=/hEfyPh \ STDERR: 2024-08-28T19:58:48.271851578Z --read-only=true \ STDERR: 2024-08-28T19:58:48.271856790Z --user=0:0 \ STDERR: 2024-08-28T19:58:48.271862030Z --rm \ STDERR: 2024-08-28T19:58:48.271867086Z --env=TMPDIR=/tmp \ STDERR: 2024-08-28T19:58:48.271872255Z --env=HOME=/hEfyPh \ STDERR: 2024-08-28T19:58:48.271877550Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/txf0dx03b5lbr_ftj/20240828195807-371422.cid \ STDERR: 2024-08-28T19:58:48.271921966Z docker.synapse.org/syn53065762/validate_score:v12 \ STDERR: 2024-08-28T19:58:48.271928172Z /bin/bash \ STDERR: 2024-08-28T19:58:48.271933498Z -c \ STDERR: 2024-08-28T19:58:48.271938973Z 'python /usr/local/bin/MIDI_validation_script/run_validation.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 && STDERR: 2024-08-28T19:58:48.271944959Z python /usr/local/bin/MIDI_validation_script/run_reports.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 # && STDERR: 2024-08-28T19:58:48.271950892Z # mkdir dciodvfy && STDERR: 2024-08-28T19:58:48.271956503Z # python /usr/local/bin/MIDI_validation_script/run_dciodvfy.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124' \ STDERR: 2024-08-28T19:58:48.271969250Z /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 STDERR: 2024-08-28T19:58:48.271975430Z Error: That compression method is not supported STDERR: 2024-08-28T19:58:48.271980978Z Error Confirming Config: [Errno 2] No such file or directory: 'config.json' STDERR: 2024-08-28T19:58:48.271986570Z Traceback (most recent call last): STDERR: 2024-08-28T19:58:48.271992103Z File "/usr/local/bin/MIDI_validation_script/run_validation.py", line 220, in STDERR: 2024-08-28T19:58:48.271998050Z main(sys.argv[1:]) STDERR: 2024-08-28T19:58:48.272020414Z File "/usr/local/bin/MIDI_validation_script/run_validation.py", line 193, in main STDERR: 2024-08-28T19:58:48.272044872Z config, config_success = check_config(config_file_path) STDERR: 2024-08-28T19:58:48.272051013Z File "/usr/local/bin/MIDI_validation_script/run_validation.py", line 176, in check_config STDERR: 2024-08-28T19:58:48.272056952Z return config, config_success STDERR: 2024-08-28T19:58:48.272062522Z UnboundLocalError: local variable 'config' referenced before assignment STDERR: 2024-08-28T19:58:48.272068423Z [job test.cwl] Max memory used: 0MiB STDERR: 2024-08-28T19:58:48.272073685Z INFO:cwltool:[job test.cwl] Max memory used: 0MiB STDERR: 2024-08-28T19:58:48.272078719Z [job test.cwl] Job error: STDERR: 2024-08-28T19:58:48.272085901Z ("Error collecting output for parameter 'database_created':\nMIDI-B-De-identification-main/steps/test.cwl:27:7: Did not find output file with glob pattern: '['results/MIDI_1_1_Testing/validation_results.db']'", {}) STDERR: 2024-08-28T19:58:48.272092771Z ERROR:cwltool:[job test.cwl] Job error: STDERR: 2024-08-28T19:58:48.272098505Z ("Error collecting output for parameter 'database_created':\nMIDI-B-De-identification-main/steps/test.cwl:27:7: Did not find output file with glob pattern: '['results/MIDI_1_1_Testing/validation_results.db']'", {}) STDERR: 2024-08-28T19:58:48.272104971Z [job test.cwl] completed permanentFail STDERR: 2024-08-28T19:58:48.272110592Z WARNING:cwltool:[job test.cwl] completed permanentFail STDERR: 2024-08-28T19:58:48.272116478Z WARNING:toil.fileStores.abstractFileStore:LOG-TO-MASTER: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-9tm9gzvl/cleanup/file-z7uhikx7/stream used 142.04% (2.8 GB [3050278912B] used, 2.0 GB [2147483648B] requested) at the end of its run. STDERR: 2024-08-28T19:58:48.272123243Z Traceback (most recent call last): STDERR: 2024-08-28T19:58:48.272160343Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2024-08-28T19:58:48.272169843Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2024-08-28T19:58:48.272175933Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner STDERR: 2024-08-28T19:58:48.272181573Z returnValues = self._run(jobGraph, fileStore) STDERR: 2024-08-28T19:58:48.272193150Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run STDERR: 2024-08-28T19:58:48.272199792Z return self.run(fileStore) STDERR: 2024-08-28T19:58:48.272205387Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2024-08-28T19:58:48.272211082Z raise cwltool.errors.WorkflowException(status) STDERR: 2024-08-28T19:58:48.272216707Z cwltool.errors.WorkflowException: permanentFail STDERR: 2024-08-28T19:58:48.272222389Z ERROR:toil.worker:Exiting the worker because of a failed job on host 86364909acc8 STDERR: 2024-08-28T19:58:48.272229268Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx to 0 STDERR: 2024-08-28T19:58:48.272237439Z <========= STDERR: 2024-08-28T19:58:48.273193557Z 86364909acc8 2024-08-28 19:58:48,272 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx is completely failed STDERR: 2024-08-28T19:58:55.596523246Z 86364909acc8 2024-08-28 19:58:55,596 MainThread INFO toil.leader: Finished toil run with 3 failed jobs. STDERR: 2024-08-28T19:58:55.596711090Z 86364909acc8 2024-08-28 19:58:55,596 MainThread INFO toil.leader: Failed jobs at end of the run: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-y6liu2dp 'CWLWorkflow' kind-CWLWorkflow/instance-9tm9gzvl 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx STDERR: 2024-08-28T19:58:55.610636854Z Traceback (most recent call last): STDERR: 2024-08-28T19:58:55.610660908Z File "/usr/local/bin/toil-cwl-runner", line 8, in STDERR: 2024-08-28T19:58:55.610670244Z sys.exit(main()) STDERR: 2024-08-28T19:58:55.610700939Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 1691, in main STDERR: 2024-08-28T19:58:55.610711351Z outobj = toil.start(wf1) STDERR: 2024-08-28T19:58:55.610717216Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 829, in start STDERR: 2024-08-28T19:58:55.610723128Z return self._runMainLoop(rootJobGraph) STDERR: 2024-08-28T19:58:55.610739913Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 1115, in _runMainLoop STDERR: 2024-08-28T19:58:55.610746828Z return Leader(config=self.config, STDERR: 2024-08-28T19:58:55.610752159Z File "/usr/local/lib/python3.8/site-packages/toil/leader.py", line 269, in run STDERR: 2024-08-28T19:58:55.610757709Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2024-08-28T19:58:55.610989867Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/tmpcirubp24' contains 3 failed jobs: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.1_cwl_get_submission.cwl/instance-y6liu2dp, 'CWLWorkflow' kind-CWLWorkflow/instance-9tm9gzvl, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx STDERR: 2024-08-28T19:58:55.611006350Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx follows: STDERR: 2024-08-28T19:58:55.611013824Z =========> STDERR: 2024-08-28T19:58:55.611019487Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2024-08-28T19:58:55.611024932Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2024-08-28T19:58:55.611050867Z [job test.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2024-08-28T19:58:55.611059913Z WARNING:cwltool:[job test.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2024-08-28T19:58:55.611066333Z [job test.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tg_31agt3/tmp-outfrh1rggt$ docker \ STDERR: 2024-08-28T19:58:55.611073065Z run \ STDERR: 2024-08-28T19:58:55.611078740Z -i \ STDERR: 2024-08-28T19:58:55.611086145Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tg_31agt3/tmp-outfrh1rggt,target=/hEfyPh \ STDERR: 2024-08-28T19:58:55.611093487Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/txf0dx03b4dpmyuzm,target=/tmp \ STDERR: 2024-08-28T19:58:55.611108173Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tmpabgei983.tmp,target=/var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124,readonly \ STDERR: 2024-08-28T19:58:55.611116231Z --workdir=/hEfyPh \ STDERR: 2024-08-28T19:58:55.611121833Z --read-only=true \ STDERR: 2024-08-28T19:58:55.611127527Z --user=0:0 \ STDERR: 2024-08-28T19:58:55.611133254Z --rm \ STDERR: 2024-08-28T19:58:55.611138782Z --env=TMPDIR=/tmp \ STDERR: 2024-08-28T19:58:55.611144335Z --env=HOME=/hEfyPh \ STDERR: 2024-08-28T19:58:55.611150047Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/txf0dx03b5lbr_ftj/20240828195807-371422.cid \ STDERR: 2024-08-28T19:58:55.611156786Z docker.synapse.org/syn53065762/validate_score:v12 \ STDERR: 2024-08-28T19:58:55.611162663Z /bin/bash \ STDERR: 2024-08-28T19:58:55.611168341Z -c \ STDERR: 2024-08-28T19:58:55.611174088Z 'python /usr/local/bin/MIDI_validation_script/run_validation.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 && STDERR: 2024-08-28T19:58:55.611180450Z python /usr/local/bin/MIDI_validation_script/run_reports.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 # && STDERR: 2024-08-28T19:58:55.611186616Z # mkdir dciodvfy && STDERR: 2024-08-28T19:58:55.611192393Z # python /usr/local/bin/MIDI_validation_script/run_dciodvfy.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124' \ STDERR: 2024-08-28T19:58:55.611198603Z /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 STDERR: 2024-08-28T19:58:55.611205345Z INFO:cwltool:[job test.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tg_31agt3/tmp-outfrh1rggt$ docker \ STDERR: 2024-08-28T19:58:55.611212143Z run \ STDERR: 2024-08-28T19:58:55.611218011Z -i \ STDERR: 2024-08-28T19:58:55.611223882Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tg_31agt3/tmp-outfrh1rggt,target=/hEfyPh \ STDERR: 2024-08-28T19:58:55.611230651Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/txf0dx03b4dpmyuzm,target=/tmp \ STDERR: 2024-08-28T19:58:55.611238024Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/tmpabgei983.tmp,target=/var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124,readonly \ STDERR: 2024-08-28T19:58:55.611249995Z --workdir=/hEfyPh \ STDERR: 2024-08-28T19:58:55.611256146Z --read-only=true \ STDERR: 2024-08-28T19:58:55.611261373Z --user=0:0 \ STDERR: 2024-08-28T19:58:55.611266894Z --rm \ STDERR: 2024-08-28T19:58:55.611272227Z --env=TMPDIR=/tmp \ STDERR: 2024-08-28T19:58:55.611277714Z --env=HOME=/hEfyPh \ STDERR: 2024-08-28T19:58:55.611283133Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/node-cf56c032-0f45-421c-854d-a0f219a43a7a-1cc402dd0e11d5ae18db04a6de87223d/tmpmm520m36/75f99c56-45b5-4325-a378-fdec3ecd1595/txf0dx03b5lbr_ftj/20240828195807-371422.cid \ STDERR: 2024-08-28T19:58:55.611288968Z docker.synapse.org/syn53065762/validate_score:v12 \ STDERR: 2024-08-28T19:58:55.611294387Z /bin/bash \ STDERR: 2024-08-28T19:58:55.611299266Z -c \ STDERR: 2024-08-28T19:58:55.611304413Z 'python /usr/local/bin/MIDI_validation_script/run_validation.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 && STDERR: 2024-08-28T19:58:55.611310254Z python /usr/local/bin/MIDI_validation_script/run_reports.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 # && STDERR: 2024-08-28T19:58:55.611315991Z # mkdir dciodvfy && STDERR: 2024-08-28T19:58:55.611322557Z # python /usr/local/bin/MIDI_validation_script/run_dciodvfy.py /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124' \ STDERR: 2024-08-28T19:58:55.611329019Z /var/lib/cwl/stg63a3fb82-20ac-4e38-afd2-16a74c6d16be/submission-9749124 STDERR: 2024-08-28T19:58:55.611334469Z Error: That compression method is not supported STDERR: 2024-08-28T19:58:55.611339749Z Error Confirming Config: [Errno 2] No such file or directory: 'config.json' STDERR: 2024-08-28T19:58:55.611345579Z Traceback (most recent call last): STDERR: 2024-08-28T19:58:55.611351246Z File "/usr/local/bin/MIDI_validation_script/run_validation.py", line 220, in STDERR: 2024-08-28T19:58:55.611356944Z main(sys.argv[1:]) STDERR: 2024-08-28T19:58:55.611362107Z File "/usr/local/bin/MIDI_validation_script/run_validation.py", line 193, in main STDERR: 2024-08-28T19:58:55.611367545Z config, config_success = check_config(config_file_path) STDERR: 2024-08-28T19:58:55.611373004Z File "/usr/local/bin/MIDI_validation_script/run_validation.py", line 176, in check_config STDERR: 2024-08-28T19:58:55.611378654Z return config, config_success STDERR: 2024-08-28T19:58:55.611384157Z UnboundLocalError: local variable 'config' referenced before assignment STDERR: 2024-08-28T19:58:55.611389567Z [job test.cwl] Max memory used: 0MiB STDERR: 2024-08-28T19:58:55.611394526Z INFO:cwltool:[job test.cwl] Max memory used: 0MiB STDERR: 2024-08-28T19:58:55.611404774Z [job test.cwl] Job error: STDERR: 2024-08-28T19:58:55.611411102Z ("Error collecting output for parameter 'database_created':\nMIDI-B-De-identification-main/steps/test.cwl:27:7: Did not find output file with glob pattern: '['results/MIDI_1_1_Testing/validation_results.db']'", {}) STDERR: 2024-08-28T19:58:55.611417090Z ERROR:cwltool:[job test.cwl] Job error: STDERR: 2024-08-28T19:58:55.611422153Z ("Error collecting output for parameter 'database_created':\nMIDI-B-De-identification-main/steps/test.cwl:27:7: Did not find output file with glob pattern: '['results/MIDI_1_1_Testing/validation_results.db']'", {}) STDERR: 2024-08-28T19:58:55.611427740Z [job test.cwl] completed permanentFail STDERR: 2024-08-28T19:58:55.611432986Z WARNING:cwltool:[job test.cwl] completed permanentFail STDERR: 2024-08-28T19:58:55.611438193Z WARNING:toil.fileStores.abstractFileStore:LOG-TO-MASTER: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-9tm9gzvl/cleanup/file-z7uhikx7/stream used 142.04% (2.8 GB [3050278912B] used, 2.0 GB [2147483648B] requested) at the end of its run. STDERR: 2024-08-28T19:58:55.611444023Z Traceback (most recent call last): STDERR: 2024-08-28T19:58:55.611449047Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2024-08-28T19:58:55.611454831Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2024-08-28T19:58:55.611461446Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner STDERR: 2024-08-28T19:58:55.611466795Z returnValues = self._run(jobGraph, fileStore) STDERR: 2024-08-28T19:58:55.611471930Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run STDERR: 2024-08-28T19:58:55.611477196Z return self.run(fileStore) STDERR: 2024-08-28T19:58:55.611482470Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2024-08-28T19:58:55.611488031Z raise cwltool.errors.WorkflowException(status) STDERR: 2024-08-28T19:58:55.611493096Z cwltool.errors.WorkflowException: permanentFail STDERR: 2024-08-28T19:58:55.611498791Z ERROR:toil.worker:Exiting the worker because of a failed job on host 86364909acc8 STDERR: 2024-08-28T19:58:55.611504338Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9bad5461-467a-485b-b856-a583327454e4/MIDI-B-De-identification-main/steps/test.cwl' /bin/bash -c kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9bad5461-467a-485b-b856-a583327454e4_MIDI-B-De-identification-main_steps_test.cwl/instance-efw22qgx to 0 STDERR: 2024-08-28T19:58:55.611671030Z <========= ```